PatternHunter
- Commercial general homology search software significantly faster than BLAST.
- http://www.bioinformaticssolutions.com/products/ph/

mreps : maximal tandem repeats search
- Open source tool for identifying serial repeats (tandem repeats) in DNA sequences.
- http://bioinfo.lifl.fr/mreps/

Interactive Blast Query
- Utility for online manipulation of Blast results. Results organized in a table format.
- http://www.aridolan.com/biq/Query.aspx

ESPript
- Formating of multiple sequence alignments to a color postscript file. Can include graphical features by using PDB entry.
- http://prodes.toulouse.inra.fr/ESPript/ESPript/index.php

Sequence Alignment and Modeling System
- Implementation of hidden Markov models for sequence analysis. Free UNIX software for nonprofit groups, and sequences can be submitted online.
- http://www.cse.ucsc.edu/research/compbio/sam.html

GWBLAST
- Genome-Wide BLAST search for similarity searching against genes or proteins. Integrated with multiple alignments and phylogenetic tree capabilities.
- http://www.imtech.res.in/raghava/gwblast/

HMM library for all proteins of known structure
- This is a server for structural superfamily assignments to protein sequences using Hidden Markov Models. The services included are: -homology searching -alignments -genome assignments
- http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/

The ISREC Group Servers
- Detection and assessment of similarity between distantly related sequences by means of a variety of remotely-executable software - from the Swiss Inst. for Experimental Cancer Research.
- http://www.isrec.isb-sib.ch/

Meta-MEME
- Software toolkit for building and using motif-based hidden Markov models of DNA and proteins - from the Univ. of California-San Diego.
- http://metameme.sdsc.edu/

GeneMatcher
- Access to Smith-Waterman-based FDF sequence comparison program, with excellent explanation of when to use it vs. BLAST - from the Univ. of Lausanne, FR.
- http://www.ch.embnet.org/software/GMFDF_form.html

BLAST
- NCBI's sequence similarity search tool designed to support analysis of nucleotide and protein databases.
- http://www.ncbi.nlm.nih.gov/BLAST/

WU-BLAST Archives
- Sensitive, selective, and rapid sequence database searching with gapped alignments - from Washington Univ.-St.Louis.
- http://blast.wustl.edu